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. 2020 Oct 22;11:5347. doi: 10.1038/s41467-020-19185-y

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© The Author(s) 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — (1) Timed phylogeny, identical to that in Fig. 1, but represented vertically. (2) The seventh pandemic V. cholerae O1 El Tor (7PET) sublineages are indicated. The names of the European and European/African sublineages are indicated by a one-digit number within or next to the blue line and corresponding to that found in the sublineage name (e.g., 1 for EUR1, 2 for EUR2/AFR3, etc). The antimicrobial resistance (AMR) phenotype for 10 antibiotics, the presence of chromosomal AMR genes (4), and genomic islands encoding AMR (5) are shown for each isolate, according to its position in the phylogeny. More detail about the genes and genomic islands encoding AMR is provided in the footnotes of Table 3. The abbreviations used for the antibiotics are as follows: STR streptomycin; SUL sulfonamides; O129 vibriostatic agent O/129; SXT trimethoprim-sulfamethoxazole; CHL chloramphenicol; TET tetracycline; FUR furazolidone; NAL nalidixic acid; PB polymyxin B; CS colistin. Note that 18 European isolates identified as outliers (Supplementary Data 1) are not represented in this timed phylogeny.